0s autopkgtest [19:46:10]: starting date and time: 2024-11-13 19:46:10+0000 0s autopkgtest [19:46:10]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [19:46:10]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m2lebio5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade pyfastx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-8.secgroup --name adt-plucky-ppc64el-pyfastx-20241113-194610-juju-7f2275-prod-proposed-migration-environment-2-07db0666-9b09-4f15-86bb-f20eeb4f68b9 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 142s autopkgtest [19:48:32]: testbed dpkg architecture: ppc64el 142s autopkgtest [19:48:32]: testbed apt version: 2.9.8 142s autopkgtest [19:48:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 143s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 143s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [98.3 kB] 143s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 143s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 143s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [958 kB] 144s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [108 kB] 144s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [673 kB] 144s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 144s Fetched 1956 kB in 1s (1869 kB/s) 144s Reading package lists... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Calculating upgrade... 147s The following NEW packages will be installed: 147s python3.13-gdbm 147s The following packages will be upgraded: 147s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 147s libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3 147s python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail 147s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 147s Need to get 4700 kB of archives. 147s After this operation, 215 kB of additional disk space will be used. 147s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 148s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 148s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 148s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 148s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 148s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 148s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 148s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 148s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 148s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 148s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 148s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 148s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 148s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 148s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 148s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 149s Fetched 4700 kB in 1s (5673 kB/s) 149s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 149s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 149s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 149s Setting up python3-minimal (3.12.7-1) ... 149s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 149s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 149s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 149s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 149s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 149s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 149s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 150s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 150s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 150s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 150s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 150s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 150s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 150s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 150s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 150s Selecting previously unselected package python3.13-gdbm. 150s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ... 150s Unpacking python3.13-gdbm (3.13.0-2) ... 150s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ... 150s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 150s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 150s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 150s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 150s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 150s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 150s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 150s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 150s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 150s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 150s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 150s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 150s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 150s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 150s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 150s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 151s Setting up libutempter0:ppc64el (1.2.1-4) ... 151s Setting up whiptail (0.52.24-2ubuntu4) ... 151s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 151s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 151s Setting up python3.13-gdbm (3.13.0-2) ... 151s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 151s Setting up bpftrace (0.21.2-2ubuntu2) ... 151s Setting up python3 (3.12.7-1) ... 151s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 151s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 151s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 151s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 151s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 151s Processing triggers for man-db (2.12.1-3) ... 153s Processing triggers for libc-bin (2.40-1ubuntu3) ... 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 155s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 155s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 155s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 156s Reading package lists... 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Calculating upgrade... 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s autopkgtest [19:48:50]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 160s autopkgtest [19:48:50]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 162s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (dsc) [2289 B] 162s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (tar) [230 kB] 162s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (diff) [7412 B] 163s gpgv: Signature made Fri Aug 30 18:49:12 2024 UTC 163s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 163s gpgv: issuer "emollier@debian.org" 163s gpgv: Can't check signature: No public key 163s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found 163s autopkgtest [19:48:53]: testing package pyfastx version 2.1.0-2 163s autopkgtest [19:48:53]: build not needed 163s autopkgtest [19:48:53]: test run-unit-test: preparing testbed 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 165s The following additional packages will be installed: 165s libpython3.13-minimal libpython3.13-stdlib pyfastx python3-all 165s python3-importlib-metadata python3-packaging python3-pyfaidx python3-pyfastx 165s python3.13 python3.13-minimal 165s Suggested packages: 165s python3.13-venv python3.13-doc binfmt-support 165s Recommended packages: 165s python3-biopython 165s The following NEW packages will be installed: 165s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib pyfastx 165s python3-all python3-importlib-metadata python3-packaging python3-pyfaidx 165s python3-pyfastx python3.13 python3.13-minimal 165s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 6327 kB/6328 kB of archives. 165s After this operation, 26.6 MB of additional disk space will be used. 165s Get:1 /tmp/autopkgtest.32WrXk/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 165s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB] 166s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB] 166s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB] 166s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-importlib-metadata all 8.5.0-1 [20.7 kB] 166s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 166s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 166s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyfastx ppc64el 2.1.0-2 [63.1 kB] 166s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pyfastx ppc64el 2.1.0-2 [122 kB] 166s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB] 166s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B] 167s Fetched 6327 kB in 1s (6946 kB/s) 167s Selecting previously unselected package libpython3.13-minimal:ppc64el. 167s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73775 files and directories currently installed.) 167s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_ppc64el.deb ... 167s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ... 167s Selecting previously unselected package python3.13-minimal. 167s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_ppc64el.deb ... 167s Unpacking python3.13-minimal (3.13.0-2) ... 167s Selecting previously unselected package libpython3.13-stdlib:ppc64el. 167s Preparing to unpack .../02-libpython3.13-stdlib_3.13.0-2_ppc64el.deb ... 167s Unpacking libpython3.13-stdlib:ppc64el (3.13.0-2) ... 167s Selecting previously unselected package python3-importlib-metadata. 167s Preparing to unpack .../03-python3-importlib-metadata_8.5.0-1_all.deb ... 167s Unpacking python3-importlib-metadata (8.5.0-1) ... 167s Selecting previously unselected package python3-packaging. 167s Preparing to unpack .../04-python3-packaging_24.1-1_all.deb ... 167s Unpacking python3-packaging (24.1-1) ... 167s Selecting previously unselected package python3-pyfaidx. 167s Preparing to unpack .../05-python3-pyfaidx_0.8.1.3-1_all.deb ... 167s Unpacking python3-pyfaidx (0.8.1.3-1) ... 167s Selecting previously unselected package python3-pyfastx. 167s Preparing to unpack .../06-python3-pyfastx_2.1.0-2_ppc64el.deb ... 167s Unpacking python3-pyfastx (2.1.0-2) ... 167s Selecting previously unselected package pyfastx. 167s Preparing to unpack .../07-pyfastx_2.1.0-2_ppc64el.deb ... 167s Unpacking pyfastx (2.1.0-2) ... 167s Selecting previously unselected package python3.13. 167s Preparing to unpack .../08-python3.13_3.13.0-2_ppc64el.deb ... 167s Unpacking python3.13 (3.13.0-2) ... 167s Selecting previously unselected package python3-all. 167s Preparing to unpack .../09-python3-all_3.12.7-1_ppc64el.deb ... 167s Unpacking python3-all (3.12.7-1) ... 167s Selecting previously unselected package autopkgtest-satdep. 167s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 167s Unpacking autopkgtest-satdep (0) ... 167s Setting up python3-importlib-metadata (8.5.0-1) ... 167s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ... 167s Setting up python3-packaging (24.1-1) ... 168s Setting up python3.13-minimal (3.13.0-2) ... 169s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ... 169s Setting up python3-pyfaidx (0.8.1.3-1) ... 169s Setting up python3.13 (3.13.0-2) ... 170s Setting up python3-pyfastx (2.1.0-2) ... 170s Setting up python3-all (3.12.7-1) ... 170s Setting up pyfastx (2.1.0-2) ... 170s Setting up autopkgtest-satdep (0) ... 170s Processing triggers for man-db (2.12.1-3) ... 171s Processing triggers for systemd (256.5-2ubuntu4) ... 173s (Reading database ... 74607 files and directories currently installed.) 173s Removing autopkgtest-satdep (0) ... 174s autopkgtest [19:49:04]: test run-unit-test: [----------------------- 174s tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) ... ERROR 174s tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) ... ERROR 174s tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) ... ERROR 174s tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) ... ERROR 174s tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) ... ERROR 174s tests.test_read (unittest.loader._FailedTest.tests.test_read) ... ERROR 174s tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) ... ERROR 174s tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) ... ERROR 174s 174s ====================================================================== 174s ERROR: tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) 174s ---------------------------------------------------------------------- 174s ImportError: Failed to import test module: tests.test_fakeys 174s Traceback (most recent call last): 174s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 174s module = self._get_module_from_name(name) 174s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 174s __import__(name) 174s ~~~~~~~~~~^^^^^^ 174s File "/tmp/autopkgtest.32WrXk/build.WXC/src/tests/test_fakeys.py", line 3, in 174s import pyfastx 174s ModuleNotFoundError: No module named 'pyfastx' 174s 174s 174s ====================================================================== 174s ERROR: tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) 174s ---------------------------------------------------------------------- 174s ImportError: Failed to import test module: tests.test_fasta 174s Traceback (most recent call last): 174s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 174s module = self._get_module_from_name(name) 174s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 174s __import__(name) 174s ~~~~~~~~~~^^^^^^ 174s File "/tmp/autopkgtest.32WrXk/build.WXC/src/tests/test_fasta.py", line 3, in 174s import pyfastx 174s ModuleNotFoundError: No module named 'pyfastx' 174s 174s 174s ====================================================================== 174s ERROR: tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) 174s ---------------------------------------------------------------------- 174s ImportError: Failed to import test module: tests.test_fastq 174s Traceback (most recent call last): 174s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 174s module = self._get_module_from_name(name) 174s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 174s __import__(name) 174s ~~~~~~~~~~^^^^^^ 174s File "/tmp/autopkgtest.32WrXk/build.WXC/src/tests/test_fastq.py", line 3, in 174s import pyfastx 174s ModuleNotFoundError: No module named 'pyfastx' 174s 174s 174s ====================================================================== 174s ERROR: tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) 174s ---------------------------------------------------------------------- 174s ImportError: Failed to import test module: tests.test_fastx 174s Traceback (most recent call last): 174s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 174s module = self._get_module_from_name(name) 174s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 174s __import__(name) 174s ~~~~~~~~~~^^^^^^ 174s File "/tmp/autopkgtest.32WrXk/build.WXC/src/tests/test_fastx.py", line 3, in 174s import pyfastx 174s ModuleNotFoundError: No module named 'pyfastx' 174s 174s 174s ====================================================================== 174s ERROR: tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) 174s ---------------------------------------------------------------------- 174s ImportError: Failed to import test module: tests.test_fqkeys 174s Traceback (most recent call last): 174s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 174s module = self._get_module_from_name(name) 174s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 174s __import__(name) 174s ~~~~~~~~~~^^^^^^ 174s File "/tmp/autopkgtest.32WrXk/build.WXC/src/tests/test_fqkeys.py", line 3, in 174s import pyfastx 174s ModuleNotFoundError: No module named 'pyfastx' 174s 174s 174s ====================================================================== 174s ERROR: tests.test_read (unittest.loader._FailedTest.tests.test_read) 174s ---------------------------------------------------------------------- 174s ImportError: Failed to import test module: tests.test_read 174s Traceback (most recent call last): 174s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 174s module = self._get_module_from_name(name) 174s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 174s __import__(name) 174s ~~~~~~~~~~^^^^^^ 174s File "/tmp/autopkgtest.32WrXk/build.WXC/src/tests/test_read.py", line 4, in 174s import pyfastx 174s ModuleNotFoundError: No module named 'pyfastx' 174s 174s 174s ====================================================================== 174s ERROR: tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) 174s ---------------------------------------------------------------------- 174s ImportError: Failed to import test module: tests.test_sequence 174s Traceback (most recent call last): 174s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 174s module = self._get_module_from_name(name) 174s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 174s __import__(name) 174s ~~~~~~~~~~^^^^^^ 174s File "/tmp/autopkgtest.32WrXk/build.WXC/src/tests/test_sequence.py", line 3, in 174s import pyfastx 174s ModuleNotFoundError: No module named 'pyfastx' 174s 174s 174s ====================================================================== 174s ERROR: tests.test_sequence_error (unittest.loader._FailedTest.tests.test_sequence_error) 174s ---------------------------------------------------------------------- 174s ImportError: Failed to import test module: tests.test_sequence_error 174s Traceback (most recent call last): 174s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 174s module = self._get_module_from_name(name) 174s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 174s __import__(name) 174s ~~~~~~~~~~^^^^^^ 174s File "/tmp/autopkgtest.32WrXk/build.WXC/src/tests/test_sequence_error.py", line 3, in 174s import pyfastx 174s ModuleNotFoundError: No module named 'pyfastx' 174s 174s 174s ---------------------------------------------------------------------- 174s Ran 8 tests in 0.001s 174s 174s FAILED (errors=8) 175s autopkgtest [19:49:05]: test run-unit-test: -----------------------] 175s run-unit-test FAIL non-zero exit status 1 175s autopkgtest [19:49:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 176s autopkgtest [19:49:06]: test test-cli: preparing testbed 294s autopkgtest [19:51:04]: testbed dpkg architecture: ppc64el 294s autopkgtest [19:51:04]: testbed apt version: 2.9.8 294s autopkgtest [19:51:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 295s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 295s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 295s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [958 kB] 296s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [98.3 kB] 296s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 296s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [108 kB] 296s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [673 kB] 296s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 296s Fetched 1956 kB in 1s (1981 kB/s) 296s Reading package lists... 298s Reading package lists... 299s Building dependency tree... 299s Reading state information... 299s Calculating upgrade... 299s The following NEW packages will be installed: 299s python3.13-gdbm 299s The following packages will be upgraded: 299s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 299s libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3 299s python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail 300s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 300s Need to get 4700 kB of archives. 300s After this operation, 215 kB of additional disk space will be used. 300s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 300s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 300s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 300s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 300s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 300s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 300s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 300s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 300s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 300s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 300s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 300s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 300s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 300s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 300s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 300s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 301s Fetched 4700 kB in 1s (6222 kB/s) 301s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 301s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 301s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 301s Setting up python3-minimal (3.12.7-1) ... 301s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 301s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 301s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 301s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 301s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 301s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 301s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 301s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 302s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 302s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 302s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 302s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 302s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 302s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 302s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 302s Selecting previously unselected package python3.13-gdbm. 302s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ... 302s Unpacking python3.13-gdbm (3.13.0-2) ... 302s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ... 302s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 302s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 302s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 302s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 302s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 302s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 302s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 302s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 302s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 302s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 302s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 302s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 302s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 302s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 302s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 302s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 302s Setting up libutempter0:ppc64el (1.2.1-4) ... 302s Setting up whiptail (0.52.24-2ubuntu4) ... 302s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 302s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 302s Setting up python3.13-gdbm (3.13.0-2) ... 302s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 302s Setting up bpftrace (0.21.2-2ubuntu2) ... 302s Setting up python3 (3.12.7-1) ... 303s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 303s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 303s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 303s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 303s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 303s Processing triggers for man-db (2.12.1-3) ... 304s Processing triggers for libc-bin (2.40-1ubuntu3) ... 305s Reading package lists... 305s Building dependency tree... 305s Reading state information... 305s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 306s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 306s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 306s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 306s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 307s Reading package lists... 307s Reading package lists... 307s Building dependency tree... 307s Reading state information... 307s Calculating upgrade... 308s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s Reading package lists... 308s Building dependency tree... 308s Reading state information... 308s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 312s Reading package lists... 312s Building dependency tree... 312s Reading state information... 312s Starting pkgProblemResolver with broken count: 0 312s Starting 2 pkgProblemResolver with broken count: 0 312s Done 313s The following additional packages will be installed: 313s pyfastx python3-importlib-metadata python3-packaging python3-pyfaidx 313s python3-pyfastx 313s Recommended packages: 313s python3-biopython 313s The following NEW packages will be installed: 313s autopkgtest-satdep pyfastx python3-importlib-metadata python3-packaging 313s python3-pyfaidx python3-pyfastx 313s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 313s Need to get 276 kB/277 kB of archives. 313s After this operation, 827 kB of additional disk space will be used. 313s Get:1 /tmp/autopkgtest.32WrXk/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 313s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-importlib-metadata all 8.5.0-1 [20.7 kB] 313s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 313s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 313s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyfastx ppc64el 2.1.0-2 [63.1 kB] 313s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pyfastx ppc64el 2.1.0-2 [122 kB] 314s Fetched 276 kB in 0s (576 kB/s) 314s Selecting previously unselected package python3-importlib-metadata. 314s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73775 files and directories currently installed.) 314s Preparing to unpack .../0-python3-importlib-metadata_8.5.0-1_all.deb ... 314s Unpacking python3-importlib-metadata (8.5.0-1) ... 314s Selecting previously unselected package python3-packaging. 314s Preparing to unpack .../1-python3-packaging_24.1-1_all.deb ... 314s Unpacking python3-packaging (24.1-1) ... 314s Selecting previously unselected package python3-pyfaidx. 314s Preparing to unpack .../2-python3-pyfaidx_0.8.1.3-1_all.deb ... 314s Unpacking python3-pyfaidx (0.8.1.3-1) ... 314s Selecting previously unselected package python3-pyfastx. 314s Preparing to unpack .../3-python3-pyfastx_2.1.0-2_ppc64el.deb ... 314s Unpacking python3-pyfastx (2.1.0-2) ... 314s Selecting previously unselected package pyfastx. 314s Preparing to unpack .../4-pyfastx_2.1.0-2_ppc64el.deb ... 314s Unpacking pyfastx (2.1.0-2) ... 314s Selecting previously unselected package autopkgtest-satdep. 314s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 314s Unpacking autopkgtest-satdep (0) ... 314s Setting up python3-importlib-metadata (8.5.0-1) ... 314s Setting up python3-packaging (24.1-1) ... 314s Setting up python3-pyfaidx (0.8.1.3-1) ... 314s Setting up python3-pyfastx (2.1.0-2) ... 314s Setting up pyfastx (2.1.0-2) ... 314s Setting up autopkgtest-satdep (0) ... 314s Processing triggers for man-db (2.12.1-3) ... 317s (Reading database ... 73872 files and directories currently installed.) 317s Removing autopkgtest-satdep (0) ... 319s autopkgtest [19:51:29]: test test-cli: [----------------------- 319s $ pyfastx --help 319s usage: pyfastx COMMAND [OPTIONS] 319s 319s A command line tool for FASTA/Q file manipulation 319s 319s options: 319s -h, --help show this help message and exit 319s -v, --version show program's version number and exit 319s 319s Commands: 319s 319s index build index for fasta/q file 319s stat show detailed statistics information of fasta/q file 319s split split fasta/q file into multiple files 319s fq2fa convert fastq file to fasta file 319s subseq get subsequences from fasta file by region 319s sample randomly sample sequences from fasta or fastq file 319s extract extract full sequences or reads from fasta/q file 319s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 319s $ pyfastx index --help 319s usage: pyfastx index [-h] [-f] fastx [fastx ...] 319s 319s positional arguments: 319s fastx fasta or fastq file, gzip support 319s 319s options: 319s -h, --help show this help message and exit 319s -f, --full build full index, base composition will be calculated 319s $ pyfastx stat --help 319s usage: pyfastx stat [-h] fastx [fastx ...] 319s 319s positional arguments: 319s fastx fasta or fastq file, gzip support 319s 319s options: 319s -h, --help show this help message and exit 319s $ pyfastx split --help 319s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 319s 319s positional arguments: 319s fastx fasta or fastq file, gzip support 319s 319s options: 319s -h, --help show this help message and exit 319s -n int split a fasta/q file into N new files with even size 319s -c int split a fasta/q file into multiple files containing 319s the same sequence counts 319s -o str, --out-dir str 319s output directory, default is current folder 320s $ pyfastx fq2fa --help 320s usage: pyfastx fq2fa [-h] [-o str] fastx 320s 320s positional arguments: 320s fastx fastq file, gzip support 320s 320s options: 320s -h, --help show this help message and exit 320s -o str, --out-file str 320s output file, default: output to stdout 320s $ pyfastx subseq --help 320s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 320s 320s positional arguments: 320s fastx input fasta file, gzip support 320s region format is chr:start-end, start and end position is 320s 1-based, multiple regions were separated by space 320s 320s options: 320s -h, --help show this help message and exit 320s -r str, --region-file str 320s tab-delimited file, one region per line, both start 320s and end position are 1-based 320s -b str, --bed-file str 320s tab-delimited BED file, 0-based start position and 320s 1-based end position 320s -o str, --out-file str 320s output file, default: output to stdout 320s $ pyfastx sample --help 320s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 320s [-o str] 320s fastx 320s 320s positional arguments: 320s fastx fasta or fastq file, gzip support 320s 320s options: 320s -h, --help show this help message and exit 320s -n int number of sequences to be sampled 320s -p float proportion of sequences to be sampled, 0~1 320s -s int, --seed int random seed, default is the current system time 320s --sequential-read start sequential reading, particularly suitable for 320s sampling large numbers of sequences 320s -o str, --out-file str 320s output file, default: output to stdout 320s $ pyfastx extract --help 320s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 320s [-o str] [--sequential-read] 320s fastx [name ...] 320s 320s positional arguments: 320s fastx fasta or fastq file, gzip support 320s name sequence name or read name, multiple names were 320s separated by space 320s 320s options: 320s -h, --help show this help message and exit 320s -l str, --list-file str 320s a file containing sequence or read names, one name per 320s line 320s --reverse-complement output reverse complement sequence 320s --out-fasta output fasta format when extract reads from fastq, 320s default output fastq format 320s -o str, --out-file str 320s output file, default: output to stdout 320s --sequential-read start sequential reading, particularly suitable for 320s extracting large numbers of sequences 320s $ pyfastx --version 320s pyfastx version 2.1.0 320s $ pyfastx index protein.fa 320s $ pyfastx index rna.fa 320s $ pyfastx index test.fa 320s $ pyfastx index test.fq 321s $ pyfastx index test.fa.gz 321s $ pyfastx index test.fq.gz 321s $ pyfastx stat protein.fa 321s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 321s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 321s $ pyfastx split -n 2 protein.fa 321s $ pyfastx fq2fa test.fq -o test.fa 321s $ pyfastx subseq protein.fa UPI0000000011:1-4 321s >UPI0000000011:1-4 321s MVDA 321s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 322s $ pyfastx extract protein.fa UPI0000000011 322s >UPI0000000011 status=active 322s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 322s IPGTIILYATYVKSLLMKS 322s autopkgtest [19:51:32]: test test-cli: -----------------------] 322s test-cli PASS 322s autopkgtest [19:51:32]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 323s autopkgtest [19:51:33]: @@@@@@@@@@@@@@@@@@@@ summary 323s run-unit-test FAIL non-zero exit status 1 323s test-cli PASS 327s virt: nova [W] Using flock in prodstack6-ppc64el 327s virt: Creating nova instance adt-plucky-ppc64el-pyfastx-20241113-194610-juju-7f2275-prod-proposed-migration-environment-2-07db0666-9b09-4f15-86bb-f20eeb4f68b9 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)... 327s virt: nova [W] Using flock in prodstack6-ppc64el 327s virt: flock: timeout while waiting to get lock 327s virt: Creating nova instance adt-plucky-ppc64el-pyfastx-20241113-194610-juju-7f2275-prod-proposed-migration-environment-2-07db0666-9b09-4f15-86bb-f20eeb4f68b9 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...